Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 851 to 900 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
213 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Divided 1 4446.72 5553.79 1.24896
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Subtracted 0 1217.96 1367.88 149.92
214 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 1217.92 1367.83 149.91
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 1 7711.36 6265.79 1445.57
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Divided 0 13174.7 15605.1 1.18447
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 1 4074.83 5086.49 1.24827
215 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Subtracted 0 1658.23 1805.52 147.29
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 1 7711.31 6265.76 1445.55
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Divided 16074 12888.4 1.24717
zinc finger protein 277. [swissprot;acc:q9nrm2] 0 13174.7 15605.1 1.18447
216 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 12478 14756 1.18256
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Subtracted 1658.07 1805.36 147.29
enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 1 10067.9 11511 1443.1
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Divided 16071.6 12886.8 1.24714
217 60s ribosomal protein l12. [swissprot;acc:p30050] Subtracted 0 1657.78 1805.05 147.27
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 1 6417.18 7859.6 1442.42
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Divided 16071.6 12886.8 1.24714
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 0 903.967 771.309 1.17199
218 keratin associated protein 9.2. [refseq;acc:nm_031961] Subtracted 1225.47 1079.01 146.46
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 1 6417.18 7859.6 1442.42
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Divided 16070.4 12886 1.24712
tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] 0 3645.5 3118.3 1.16907
219 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 8852.4 7572.88 1.16896
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Subtracted 10 156 146
transforming protein n-ras. [swissprot;acc:p01111] Divided 1 16069.8 12885.6 1.24711
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Subtracted 6417.18 7859.6 1442.42
220 crk-like protein. [swissprot;acc:p46109]
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 0 326.677 472.605 145.928
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Divided 1 41482.5 33356.5 1.24361
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 0 18704 21730 1.16178
221 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 1 41482.5 33356.5 1.24361
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Subtracted 0 1225.09 1079.36 145.73
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 1 6417.18 7859.6 1442.42
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Divided 0 1905.84 1643 1.15998
222 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 1499.4 1735.23 1.15728
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1 41482.5 33356.5 1.24361
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Subtracted 0 1225.09 1079.36 145.73
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 1 6417.18 7859.6 1442.42
223 cytohesin 4. [swissprot;acc:q9uia0] Divided 41482.5 33356.5 1.24361
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 0 750.981 650.724 1.15407
keratin associated protein 1.5. [refseq;acc:nm_031957] Subtracted 1225.09 1079.36 145.73
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 1 6417.18 7859.59 1442.41
224 60s ribosomal protein l7. [swissprot;acc:p18124] Divided 0 1915.27 2206.07 1.15183
cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 1 41482.5 33356.5 1.24361
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Subtracted 0 1225.09 1079.36 145.73
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 1 6417.18 7859.59 1442.41
225 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] 6417.19 7859.51 1442.32
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 0 1225.09 1079.36 145.73
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Divided 1 9035 7279.6 1.24114
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 0 8763 7608 1.15181

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/